SAXSdb — 3nem

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Aspartyl-tRNA synthetase

Thermococcus kodakarensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYD_PYRKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 1–438 Author chain B； PDBConstruct 1–438； UniProt 1–438

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3nem
Deposition date deposition_date	2010-06-09
Structure title title	Aspartyl-tRNA synthetase complexed with aspartyl adenylate
Keywords keywords	Rossmann Fold, OB Fold, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3nem__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3nem__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nem__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	29.91 Å
Rg (electron density)	29.38 Å
Total Rg	30.16 Å
Atom count	7251
Residues	876
Excluded volume	129590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nem__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Aspartyl-tRNA synthetase
Molecular weight formula_weight	50979.4 kDa
EC 编号 ec_number	6.1.1.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7724

MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLDNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAQSPQLYKQIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP

Source Source

Source organism organism	Thermococcus kodakarensis
Common name common_name	Thermococcus kodakaraensis
NCBI taxonomy ID ncbi_taxonomy_id	311400
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	462.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	473

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3nema1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.0 — automated matches

Domain ID domain_id	d3nema2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.0 — automated matches

Domain ID domain_id	d3nemb1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.0 — automated matches

Domain ID domain_id	d3nemb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3nemA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3nemA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	3nemB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3nemB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

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Unit-cell length a length_a	123.220 Å
Unit-cell length b length_b	124.870 Å
Unit-cell length c length_c	86.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	28.580 Å
R factor r_factor	—
R_work r_work	0.1880
R_free r_free	0.2130

Aspartyl-tRNA synthetase complexed with aspartyl adenylate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Aspartyl-tRNA synthetase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3nem__assembly_1__model_1

3nem__assembly_1__model_1 | I(q)

3nem__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Aspartyl-tRNA synthetase complexed with aspartyl adenylate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Aspartyl-tRNA synthetase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3nem__assembly_1__model_1

3nem__assembly_1__model_1 | I(q)

3nem__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)